GSM6767488: intrahepatic injection alone - Control - Liver; Mus musculus; RNA-Seq
CD4/CD8 T cells were enriched by positive selection from tumor cell suspension by magnetic cell sorting. Samples were processed on the Chromium Controller using the Chromium NextGEM Single Cell 5' reagents kits v2 (Dual Index) protocol from 10x Genomics. Starting with 16000 cells per sample, 5' gene expression libraries and VDJ immune repertoire from TCR libraries were prepared according to the manufacturer's instructions. The quality of cDNA and final libraries were assessed on the 5200 Fragment Analyzer system using the HS NGS Fragment kit (1-6000bp). Libraries were quantified using the Qubit 4 fluorometer and the KAPA library quantification kit for qPCR amplification on the QuantStudio5 system. The libraries were pooled at a 1:4 ratio (VDJ library: gene expression library) per sample reaching an equimolarity of the different samples in the final sequencing pool including 1% PhiX sequencing control. The paired-end sequencing was performed on the NovaSeq 6000 system with the NovaSeq S1 Reagent kit v1.5 (100 cycles) following the cycling parameters: 26bp (read1), 10bp (index 1), 10bp (index2), 90bp (read2).